The actual model of the mother ship is on display at the Udvar-Hazey extension of the Air and Space Museum at Dulles International Airport. The plaque on the display case points out where to find not only the R2D2, but also quite a few model kit artifacts. The other one that sticks in my mind is a tiny seaplane, though I've never spotted it in the movie.

Go buy the DVD for this movie... Go ahead, I'll wait...
Now watch the documentary, it's an hour and a half... don't worry, we've got time...
You'll see a segment where the sfx crew shows you exactly where to find R2D2. Oh yeah, everybody's favorite droid is right there, hanging from his boots... or treads... whatever.

Yes you are correct, but this perhaps was a pre-tribute, cause the guy who had just finished the Star Wars visual effects worked on Close Encounters just after Star Wars was finished. Or maybe he was working on both at the same time, I don't know.

Last time I heard, there was nothing special about the underside of the space ship (nothing hidden, that is). I actually heard that the bottom of the spaceship is upside down footage of the city of Los Angeles filmed at night from the top of some hill. Dunno if it's true, but it seems to work (moving lights from cars, lights from buildings, outcroppings, etc). I'll have to check out the movie again and find out for sure.